Make sure you tell it to ignore your search indexes and other SharePoint areas!See: http://support.microsoft.com/kb/952167
To be sure it is not hitting your index location, you can check where that is currently set by:
Central Admin -> Application Management -> Manage service applications -> Search Service Application ->Search Application Topology (Modify) -> IndexPartition/Query Component (Edit Properties).
Or via PowerShell, run the SharePoint 2010 Management Shell command:
PS:http://support.microsoft.com/kb/322941 says"Microsoft strongly encourages the development and adoption of SharePoint Portal Server VS API-based antivirus solutions."but the only one I can find for SP2013 is ESET…http://www.eset.com/beta/sharepoint/
PPS: I have heard that Symantec have a SP2013 aware thing in beta. Supposedly a separate server. Will know more in a month or two.